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Egon Willighagen egonw

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@egonw
egonw / gist:26e11c4001a84e9b72095360a661c26d
Created September 3, 2022 16:13
Parsed C(=O)(C(C(C(C(C(F)(F)F)(F)F)(F)F)(F)F)(F)F)O into CDKMolecule:C6HF11O2
InChIKey match: http://www.wikidata.org/entity/Q27156874
PubChem CID match: http://www.wikidata.org/entity/Q27156874
====================
C₆HF₁₁O₂ is already in Wikidata as http://www.wikidata.org/entity/Q27156874
Full stereochemistry is defined
====================
Parsed C(=O)(C(C(C(C(C(C(F)(F)F)(F)F)(F)F)(F)F)(F)F)(F)F)O into CDKMolecule:C7HF13O2
InChIKey match: http://www.wikidata.org/entity/Q27116513
PubChem CID match: http://www.wikidata.org/entity/Q27116513
@egonw
egonw / gist:1c8bc99373a24075838ee19976c74856
Last active November 13, 2022 13:01
# tool: scholia
# / defaultView:Graph
PREFIX target: <http://www.wikidata.org/entity/Q30149558>
SELECT
?citing_work ?citing_workLabel ?grey ?padded_grey ?rgb
?cited_work ?cited_workLabel
WITH {
SELECT (COUNT(*) AS ?count) ?citing_work WHERE {
@egonw
egonw / gist:192f0f0281859897febb7286345af235
Last active September 11, 2022 10:11
SELECT ?smiles
WHERE {
SERVICE wikibase:mwapi {
bd:serviceParam wikibase:endpoint "www.wikidata.org";
wikibase:api "Search";
mwapi:srsearch "haswbstatement:P235 -haswbstatement:P274";
mwapi:srlimit "max".
?cmp wikibase:apiOutputItem mwapi:title.
}
OPTIONAL { ?cmp wdt:P2017 ?isoSmi }
@egonw
egonw / gist:083b05bbc9b5ba8fe12320a27ca2b9e0
Created August 22, 2022 10:38
SELECT DISTINCT ?doi WITH {
SELECT DISTINCT ?pub ?doi ?date WHERE {
SERVICE bd:sample { ?pub wdt:P356 ?doi . bd:serviceParam bd:sample.limit 75000 }
?pub wdt:P577 ?date .
MINUS { ?pub wdt:P2860 [] }
FILTER (year(?date) < 1900)
}
} AS %RANDOM WHERE {
SELECT DISTINCT ?pub ?doi ?date WHERE {
INCLUDE %RANDOM
@egonw
egonw / find things without chemical formula
Last active August 21, 2022 19:45
SELECT DISTINCT ?smiles WITH {
SELECT DISTINCT ?cmp ?inchikey WHERE {
SERVICE bd:sample { ?cmp wdt:P235 ?inchikey . bd:serviceParam bd:sample.limit 200000 }
MINUS { ?cmp wdt:P274 [] }
FILTER (STRENDS(STR(?inchikey), "-N"))
}
} AS %RANDOM WHERE {
SELECT DISTINCT ?smiles WHERE {
INCLUDE %RANDOM
OPTIONAL { ?cmp wdt:P233 ?canSmi }
@egonw
egonw / calculating-nano-inchis-in-python-with-the-help-of-java-bacting-and-scyjava.ipynb
Last active September 4, 2022 12:09
Calculating Nano InChIs in Python (with the help of Java, Bacting, and Scyjava)
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@egonw
egonw / lacphe.gpml
Created June 18, 2022 06:39
<?xml version="1.0" encoding="UTF-8"?>
<Pathway xmlns="http://pathvisio.org/GPML/2013a" Name="Lac-Phe pathway" Organism="Homo sapiens">
<Graphics BoardWidth="995.0" BoardHeight="592.0" />
<DataNode TextLabel="(S)-lactate" GraphId="c484a" Type="Metabolite">
<Graphics CenterX="196.0" CenterY="187.0" Width="90.0" Height="25.0" ZOrder="32768" FontSize="12" Valign="Middle" Color="3955e7" />
<Xref Database="ChEBI" ID="16651" />
</DataNode>
<DataNode TextLabel="Lac-Phe" GraphId="fcf48" Type="Metabolite">
<Graphics CenterX="376.0" CenterY="187.0" Width="90.0" Height="25.0" ZOrder="32768" FontSize="12" Valign="Middle" Color="3955e7" />
<Xref Database="ChEBI" ID="167456" />
@egonw
egonw / getBridgeDbDatabases.sh
Created February 23, 2022 19:15
Script to download BridgeDb identifier mapping databases
#!/bin/bash
wget -nc https://bridgedb.github.io/data/gene.json
wget -nc https://bridgedb.github.io/data/corona.json
wget -nc https://bridgedb.github.io/data/other.json
wget -nc https://bridgedb.github.io/data/gene.json.config
wget -nc https://bridgedb.github.io/data/corona.json.config
wget -nc https://bridgedb.github.io/data/other.json.config
@egonw
egonw / cito.nanopub
Created November 7, 2021 21:04
@prefix this: <http://purl.org/np/RAMc79WFgK30tHAeWj6PugKxfcqFsgErU2n8pLPJnwNrU> .
@prefix sub: <http://purl.org/np/RAMc79WFgK30tHAeWj6PugKxfcqFsgErU2n8pLPJnwNrU#> .
@prefix has-source: <http://semanticscience.org/resource/SIO_000253> .
@prefix wp: <http://vocabularies.wikipathways.org/wp#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix np: <http://www.nanopub.org/nschema#> .
@prefix wd: <https://www.wikidata.org/entity/> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix dc: <http://purl.org/dc/elements/1.1/> .
@egonw
egonw / smi_inchikeys.groovy
Created September 4, 2021 10:54
Convert a file with SMILES to InChIKeys
@Grab(group='org.openscience.cdk', module='cdk-bundle', version='2.5')
// Copyright (C) 2021 Egon Willighagen <0000-0001-7542-0286@orcid.org>
//
// MIT license
//
// If you use this script, please cite the CDK 2.0 article:
// https://jcheminf.biomedcentral.com/articles/10.1186/s13321-017-0220-4
import org.openscience.cdk.interfaces.*;